Genomic Epidemiology of 2023-2024 Oropouche Outbreak in Iquitos, Peru reveals independent origin from a concurrent outbreak in Brazil

Abstract

Oropouche virus is an arbovirus endemic to the Americas. Periodic outbreaks have occurred since its description in 1955. In late 2023, an outbreak occurred in Peru, centered in and around Iquitos in the Eastern Peruvian Amazon. An existing acute febrile illness (AFI) surveillance program was able to document its emergence and characterize arthralgia and dysuria and the absence of diarrhea as distinctive clinical features of Oropouche virus-associated febrile illness relative to other causes of AFI. Sequencing of isolates from the outbreak demonstrated that strains from this region were distinct from those causing disease in Brazil, despite the large-scale movement of people along the Amazon corridor, but highly similar to strains from Colombia and Ecuador. Our findings suggest that the current outbreak in South America is fundamentally multifocal in origin and not the result of geographic spread from Brazil, which experienced an outbreak between 2022 and 2024.

Keywords: acute febrile illness; arbovirus; orthobunyavirus.

Figure 1.

Time series graph of OROV detections in symptomatic and asymptomatic RIVERA subjects over the three year study period reveal sporadic detections of Oropouche in 0.4% of cases and control prior to December 2023. Between December 2023 and August 2024, Oropouche identification increased to a peak prevalence of 11% in those with acute febrile illness and 3% of asymptomatic controls in March 2024.

Figure 2.

Unrooted Maximum-likelihood (ML) tree based on the (1) 6,550 bp of the L segment; (2) 4,087 bp of the M segment; and (3) 638 bp of the S segment. Nucleotide alignments for each segment were generated using MUSCLE plugin (v5.1) in Geneious Prime (v2024.0.7). Each tree was generated using the General Time Reversible (GTR) model with gamma distributed rates and bootstrapped 10,000 times.

Figure 3.

Amino acid sequence alignment for the S (A), M (B), and L (C) segments of the Oropouche virus from Peru (2024), Colombia (2024), Ecuador (2016), Peru (1992), Cuba (2024), and Brazil (2024). The S segment has 0/212 (0%) amino acid heterogeneity, and the L segment 38/2,183 (1.74%) amino acid heterogeneity among the viruses from different countries. However, there is quite a significant amount of amino acid heterogeneity in the M segment, as it has 105/1,361 (7.71%) amino acid heterogeneity, including 30/428 (7.01%) amino acid changes in the N terminus of Gc, the region coding the antigen that is purported to mediate protective immunity.